Per chromosome imputation report for cohort C58_cohort.
Chromosome index, 23 in total. Skip to the section for a particular chromosome using the buttons below.
Information captured during the processing of this cohort.
| Property | Value |
|---|---|
| FORMAT | MINIMAC2 |
| UPLOADED | 12.4.2021 |
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 12989316 | 73.862 |
| 0.1 | 1220278 | 6.939 |
| 0.2 | 810374 | 4.608 |
| 0.3 | 619465 | 3.523 |
| 0.4 | 495044 | 2.815 |
| 0.5 | 404896 | 2.302 |
| 0.6 | 348948 | 1.984 |
| 0.7 | 290824 | 1.654 |
| 0.8 | 240831 | 1.369 |
| 0.9 | 165960 | 0.944 |
| Total | 17585936 | 100.000 |
Variants binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 878178 | 4.994 |
| 0.4 | 986205 | 5.608 |
| 0.5 | 1266433 | 7.201 |
| 0.6 | 1745532 | 9.926 |
| 0.7 | 2316549 | 13.173 |
| 0.8 | 2866924 | 16.302 |
| 0.9 | 7473260 | 42.496 |
| 1.0 | 52855 | 0.301 |
| Total | 17585936 | 100.000 |
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 986394 | 74.2386 |
| 0.1 | 90432 | 6.8062 |
| 0.2 | 57825 | 4.3521 |
| 0.3 | 45498 | 3.4243 |
| 0.4 | 37184 | 2.7986 |
| 0.5 | 30231 | 2.2753 |
| 0.6 | 27317 | 2.0560 |
| 0.7 | 21929 | 1.6504 |
| 0.8 | 18651 | 1.4037 |
| 0.9 | 13219 | 0.9949 |
| Total | 1328680 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 67228 | 5.0598 |
| 0.4 | 75101 | 5.6523 |
| 0.5 | 96921 | 7.2945 |
| 0.6 | 133319 | 10.0339 |
| 0.7 | 179751 | 13.5285 |
| 0.8 | 219483 | 16.5189 |
| 0.9 | 552893 | 41.6122 |
| 1.0 | 3984 | 0.2998 |
| Total | 1328680 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1105124 | 74.6808 |
| 0.1 | 101200 | 6.8388 |
| 0.2 | 65193 | 4.4055 |
| 0.3 | 49964 | 3.3764 |
| 0.4 | 39061 | 2.6396 |
| 0.5 | 32681 | 2.2085 |
| 0.6 | 28663 | 1.9370 |
| 0.7 | 23142 | 1.5639 |
| 0.8 | 20272 | 1.3699 |
| 0.9 | 14497 | 0.9797 |
| Total | 1479797 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 68964 | 4.6604 |
| 0.4 | 77064 | 5.2077 |
| 0.5 | 99543 | 6.7268 |
| 0.6 | 142105 | 9.6030 |
| 0.7 | 195576 | 13.2164 |
| 0.8 | 242376 | 16.3790 |
| 0.9 | 649661 | 43.9020 |
| 1.0 | 4508 | 0.3046 |
| Total | 1479797 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 915800 | 73.9198 |
| 0.1 | 87495 | 7.0623 |
| 0.2 | 55668 | 4.4933 |
| 0.3 | 42477 | 3.4286 |
| 0.4 | 35295 | 2.8489 |
| 0.5 | 29045 | 2.3444 |
| 0.6 | 24752 | 1.9979 |
| 0.7 | 20362 | 1.6435 |
| 0.8 | 16625 | 1.3419 |
| 0.9 | 11392 | 0.9195 |
| Total | 1238911 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 56462 | 4.5574 |
| 0.4 | 62799 | 5.0689 |
| 0.5 | 83462 | 6.7367 |
| 0.6 | 119177 | 9.6195 |
| 0.7 | 162192 | 13.0915 |
| 0.8 | 205301 | 16.5711 |
| 0.9 | 546140 | 44.0823 |
| 1.0 | 3378 | 0.2727 |
| Total | 1238911 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 899611 | 73.2200 |
| 0.1 | 81623 | 6.6434 |
| 0.2 | 61054 | 4.9692 |
| 0.3 | 45890 | 3.7350 |
| 0.4 | 32970 | 2.6835 |
| 0.5 | 27692 | 2.2539 |
| 0.6 | 24465 | 1.9912 |
| 0.7 | 21592 | 1.7574 |
| 0.8 | 19906 | 1.6202 |
| 0.9 | 13838 | 1.1263 |
| Total | 1228641 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 56355 | 4.5868 |
| 0.4 | 63463 | 5.1653 |
| 0.5 | 82698 | 6.7309 |
| 0.6 | 118447 | 9.6405 |
| 0.7 | 159639 | 12.9931 |
| 0.8 | 200990 | 16.3587 |
| 0.9 | 543008 | 44.1958 |
| 1.0 | 4041 | 0.3289 |
| Total | 1228641 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 838247 | 74.1976 |
| 0.1 | 76469 | 6.7687 |
| 0.2 | 52586 | 4.6547 |
| 0.3 | 40412 | 3.5771 |
| 0.4 | 31572 | 2.7946 |
| 0.5 | 25058 | 2.2180 |
| 0.6 | 22023 | 1.9494 |
| 0.7 | 18234 | 1.6140 |
| 0.8 | 14947 | 1.3230 |
| 0.9 | 10202 | 0.9030 |
| Total | 1129750 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 52095 | 4.6112 |
| 0.4 | 56869 | 5.0338 |
| 0.5 | 73670 | 6.5209 |
| 0.6 | 104981 | 9.2924 |
| 0.7 | 146100 | 12.9321 |
| 0.8 | 182520 | 16.1558 |
| 0.9 | 509734 | 45.1192 |
| 1.0 | 3781 | 0.3347 |
| Total | 1129750 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 820483 | 73.3437 |
| 0.1 | 81743 | 7.3071 |
| 0.2 | 53221 | 4.7575 |
| 0.3 | 40093 | 3.5839 |
| 0.4 | 32568 | 2.9113 |
| 0.5 | 26248 | 2.3463 |
| 0.6 | 22229 | 1.9871 |
| 0.7 | 17244 | 1.5415 |
| 0.8 | 15082 | 1.3482 |
| 0.9 | 9771 | 0.8734 |
| Total | 1118682 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 46574 | 4.1633 |
| 0.4 | 51520 | 4.6054 |
| 0.5 | 66963 | 5.9859 |
| 0.6 | 97798 | 8.7423 |
| 0.7 | 136853 | 12.2334 |
| 0.8 | 177917 | 15.9042 |
| 0.9 | 536814 | 47.9863 |
| 1.0 | 4243 | 0.3793 |
| Total | 1118682 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 734353 | 73.8108 |
| 0.1 | 68392 | 6.8742 |
| 0.2 | 47912 | 4.8157 |
| 0.3 | 35464 | 3.5645 |
| 0.4 | 28995 | 2.9143 |
| 0.5 | 22765 | 2.2881 |
| 0.6 | 19592 | 1.9692 |
| 0.7 | 16384 | 1.6468 |
| 0.8 | 12193 | 1.2255 |
| 0.9 | 8862 | 0.8907 |
| Total | 994912 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 48675 | 4.8924 |
| 0.4 | 55316 | 5.5599 |
| 0.5 | 71153 | 7.1517 |
| 0.6 | 97372 | 9.7870 |
| 0.7 | 131513 | 13.2186 |
| 0.8 | 163194 | 16.4029 |
| 0.9 | 424660 | 42.6832 |
| 1.0 | 3029 | 0.3044 |
| Total | 994912 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 734130 | 74.8050 |
| 0.1 | 64590 | 6.5815 |
| 0.2 | 44322 | 4.5162 |
| 0.3 | 32103 | 3.2712 |
| 0.4 | 27834 | 2.8362 |
| 0.5 | 21463 | 2.1870 |
| 0.6 | 19264 | 1.9629 |
| 0.7 | 15431 | 1.5724 |
| 0.8 | 13291 | 1.3543 |
| 0.9 | 8964 | 0.9134 |
| Total | 981392 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 46657 | 4.7542 |
| 0.4 | 50100 | 5.1050 |
| 0.5 | 64053 | 6.5267 |
| 0.6 | 89582 | 9.1281 |
| 0.7 | 125687 | 12.8070 |
| 0.8 | 160138 | 16.3174 |
| 0.9 | 441681 | 45.0056 |
| 1.0 | 3494 | 0.3560 |
| Total | 981392 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 549040 | 74.1109 |
| 0.1 | 53660 | 7.2432 |
| 0.2 | 33824 | 4.5657 |
| 0.3 | 24869 | 3.3569 |
| 0.4 | 20426 | 2.7572 |
| 0.5 | 15830 | 2.1368 |
| 0.6 | 14587 | 1.9690 |
| 0.7 | 11508 | 1.5534 |
| 0.8 | 9733 | 1.3138 |
| 0.9 | 7359 | 0.9933 |
| Total | 740836 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 33751 | 4.5558 |
| 0.4 | 38437 | 5.1883 |
| 0.5 | 49310 | 6.6560 |
| 0.6 | 71244 | 9.6167 |
| 0.7 | 96990 | 13.0920 |
| 0.8 | 125133 | 16.8908 |
| 0.9 | 323692 | 43.6928 |
| 1.0 | 2279 | 0.3076 |
| Total | 740836 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 640299 | 73.8074 |
| 0.1 | 60590 | 6.9842 |
| 0.2 | 40007 | 4.6116 |
| 0.3 | 28830 | 3.3232 |
| 0.4 | 24549 | 2.8298 |
| 0.5 | 21032 | 2.4244 |
| 0.6 | 16985 | 1.9579 |
| 0.7 | 14019 | 1.6160 |
| 0.8 | 12634 | 1.4563 |
| 0.9 | 8582 | 0.9892 |
| Total | 867527 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 38225 | 4.4062 |
| 0.4 | 41827 | 4.8214 |
| 0.5 | 54270 | 6.2557 |
| 0.6 | 77626 | 8.9480 |
| 0.7 | 110188 | 12.7014 |
| 0.8 | 141187 | 16.2747 |
| 0.9 | 400902 | 46.2120 |
| 1.0 | 3302 | 0.3806 |
| Total | 867527 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 637097 | 73.8688 |
| 0.1 | 59299 | 6.8755 |
| 0.2 | 36089 | 4.1844 |
| 0.3 | 31350 | 3.6349 |
| 0.4 | 24172 | 2.8026 |
| 0.5 | 20571 | 2.3851 |
| 0.6 | 17941 | 2.0802 |
| 0.7 | 14654 | 1.6991 |
| 0.8 | 12104 | 1.4034 |
| 0.9 | 9194 | 1.0660 |
| Total | 862471 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 39297 | 4.5563 |
| 0.4 | 43955 | 5.0964 |
| 0.5 | 58881 | 6.8270 |
| 0.6 | 83303 | 9.6586 |
| 0.7 | 111944 | 12.9795 |
| 0.8 | 138611 | 16.0714 |
| 0.9 | 383120 | 44.4212 |
| 1.0 | 3360 | 0.3896 |
| Total | 862471 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 608619 | 74.0255 |
| 0.1 | 56144 | 6.8287 |
| 0.2 | 35865 | 4.3622 |
| 0.3 | 30535 | 3.7139 |
| 0.4 | 22842 | 2.7782 |
| 0.5 | 19023 | 2.3137 |
| 0.6 | 15965 | 1.9418 |
| 0.7 | 12754 | 1.5513 |
| 0.8 | 12144 | 1.4771 |
| 0.9 | 8284 | 1.0076 |
| Total | 822175 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 38966 | 4.7394 |
| 0.4 | 43151 | 5.2484 |
| 0.5 | 54424 | 6.6195 |
| 0.6 | 78149 | 9.5052 |
| 0.7 | 106316 | 12.9311 |
| 0.8 | 133715 | 16.2636 |
| 0.9 | 364365 | 44.3172 |
| 1.0 | 3089 | 0.3757 |
| Total | 822175 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 447875 | 72.6822 |
| 0.1 | 42894 | 6.9609 |
| 0.2 | 27927 | 4.5321 |
| 0.3 | 22725 | 3.6879 |
| 0.4 | 17572 | 2.8516 |
| 0.5 | 15582 | 2.5287 |
| 0.6 | 12357 | 2.0053 |
| 0.7 | 11510 | 1.8679 |
| 0.8 | 9702 | 1.5745 |
| 0.9 | 8066 | 1.3090 |
| Total | 616210 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 26665 | 4.3273 |
| 0.4 | 29732 | 4.8250 |
| 0.5 | 39135 | 6.3509 |
| 0.6 | 57535 | 9.3369 |
| 0.7 | 81419 | 13.2129 |
| 0.8 | 102499 | 16.6338 |
| 0.9 | 277374 | 45.0129 |
| 1.0 | 1851 | 0.3004 |
| Total | 616210 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 411335 | 74.1691 |
| 0.1 | 38932 | 7.0199 |
| 0.2 | 25809 | 4.6537 |
| 0.3 | 18632 | 3.3596 |
| 0.4 | 15214 | 2.7433 |
| 0.5 | 11798 | 2.1273 |
| 0.6 | 10149 | 1.8300 |
| 0.7 | 8974 | 1.6181 |
| 0.8 | 7931 | 1.4301 |
| 0.9 | 5817 | 1.0489 |
| Total | 554591 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 26757 | 4.8246 |
| 0.4 | 31134 | 5.6139 |
| 0.5 | 40126 | 7.2352 |
| 0.6 | 55908 | 10.0809 |
| 0.7 | 73530 | 13.2584 |
| 0.8 | 90195 | 16.2633 |
| 0.9 | 235585 | 42.4791 |
| 1.0 | 1356 | 0.2445 |
| Total | 554591 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 359555 | 73.8675 |
| 0.1 | 33501 | 6.8825 |
| 0.2 | 22036 | 4.5271 |
| 0.3 | 16902 | 3.4724 |
| 0.4 | 14245 | 2.9265 |
| 0.5 | 11855 | 2.4355 |
| 0.6 | 8931 | 1.8348 |
| 0.7 | 7894 | 1.6218 |
| 0.8 | 6540 | 1.3436 |
| 0.9 | 5298 | 1.0884 |
| Total | 486757 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 25315 | 5.2007 |
| 0.4 | 29390 | 6.0379 |
| 0.5 | 37672 | 7.7394 |
| 0.6 | 51238 | 10.5264 |
| 0.7 | 66441 | 13.6497 |
| 0.8 | 80703 | 16.5797 |
| 0.9 | 195061 | 40.0736 |
| 1.0 | 937 | 0.1925 |
| Total | 486757 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 386348 | 73.9108 |
| 0.1 | 37568 | 7.1870 |
| 0.2 | 22742 | 4.3507 |
| 0.3 | 19133 | 3.6603 |
| 0.4 | 14402 | 2.7552 |
| 0.5 | 11934 | 2.2830 |
| 0.6 | 10809 | 2.0678 |
| 0.7 | 9383 | 1.7950 |
| 0.8 | 6355 | 1.2158 |
| 0.9 | 4048 | 0.7744 |
| Total | 522722 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 30214 | 5.7801 |
| 0.4 | 33987 | 6.5019 |
| 0.5 | 42614 | 8.1523 |
| 0.6 | 57234 | 10.9492 |
| 0.7 | 72563 | 13.8818 |
| 0.8 | 88743 | 16.9771 |
| 0.9 | 196357 | 37.5643 |
| 1.0 | 1010 | 0.1932 |
| Total | 522722 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 324184 | 73.2813 |
| 0.1 | 30216 | 6.8303 |
| 0.2 | 22791 | 5.1519 |
| 0.3 | 15592 | 3.5245 |
| 0.4 | 13546 | 3.0621 |
| 0.5 | 11043 | 2.4963 |
| 0.6 | 9038 | 2.0430 |
| 0.7 | 7830 | 1.7700 |
| 0.8 | 5609 | 1.2679 |
| 0.9 | 2534 | 0.5728 |
| Total | 442383 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 32804 | 7.4153 |
| 0.4 | 36722 | 8.3010 |
| 0.5 | 46096 | 10.4199 |
| 0.6 | 54933 | 12.4175 |
| 0.7 | 63323 | 14.3141 |
| 0.8 | 71600 | 16.1851 |
| 0.9 | 136104 | 30.7661 |
| 1.0 | 801 | 0.1811 |
| Total | 442383 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 356306 | 73.3741 |
| 0.1 | 33896 | 6.9802 |
| 0.2 | 23587 | 4.8573 |
| 0.3 | 17667 | 3.6382 |
| 0.4 | 13960 | 2.8748 |
| 0.5 | 10918 | 2.2483 |
| 0.6 | 9458 | 1.9477 |
| 0.7 | 8078 | 1.6635 |
| 0.8 | 6605 | 1.3602 |
| 0.9 | 5127 | 1.0558 |
| Total | 485602 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 23576 | 4.8550 |
| 0.4 | 27000 | 5.5601 |
| 0.5 | 36697 | 7.5570 |
| 0.6 | 50731 | 10.4470 |
| 0.7 | 66687 | 13.7329 |
| 0.8 | 79666 | 16.4056 |
| 0.9 | 199973 | 41.1804 |
| 1.0 | 1272 | 0.2619 |
| Total | 485602 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 237780 | 71.4170 |
| 0.1 | 28359 | 8.5176 |
| 0.2 | 18465 | 5.5459 |
| 0.3 | 12823 | 3.8514 |
| 0.4 | 9688 | 2.9098 |
| 0.5 | 8179 | 2.4566 |
| 0.6 | 6623 | 1.9892 |
| 0.7 | 5599 | 1.6817 |
| 0.8 | 3731 | 1.1206 |
| 0.9 | 1699 | 0.5103 |
| Total | 332946 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 31189 | 9.3676 |
| 0.4 | 35471 | 10.6537 |
| 0.5 | 40058 | 12.0314 |
| 0.6 | 44010 | 13.2184 |
| 0.7 | 46341 | 13.9185 |
| 0.8 | 51010 | 15.3208 |
| 0.9 | 84529 | 25.3882 |
| 1.0 | 338 | 0.1015 |
| Total | 332946 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 280531 | 73.7578 |
| 0.1 | 26934 | 7.0815 |
| 0.2 | 18027 | 4.7397 |
| 0.3 | 13416 | 3.5274 |
| 0.4 | 11200 | 2.9447 |
| 0.5 | 8919 | 2.3450 |
| 0.6 | 7797 | 2.0500 |
| 0.7 | 5990 | 1.5749 |
| 0.8 | 4472 | 1.1758 |
| 0.9 | 3055 | 0.8032 |
| Total | 380341 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 20065 | 5.2755 |
| 0.4 | 23250 | 6.1129 |
| 0.5 | 31213 | 8.2066 |
| 0.6 | 43029 | 11.3133 |
| 0.7 | 52372 | 13.7697 |
| 0.8 | 61692 | 16.2202 |
| 0.9 | 147801 | 38.8601 |
| 1.0 | 919 | 0.2416 |
| Total | 380341 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 162735 | 71.9773 |
| 0.1 | 15954 | 7.0564 |
| 0.2 | 10228 | 4.5238 |
| 0.3 | 8986 | 3.9745 |
| 0.4 | 7157 | 3.1655 |
| 0.5 | 5947 | 2.6303 |
| 0.6 | 4930 | 2.1805 |
| 0.7 | 4447 | 1.9669 |
| 0.8 | 4010 | 1.7736 |
| 0.9 | 1698 | 0.7510 |
| Total | 226092 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 12746 | 5.6375 |
| 0.4 | 14374 | 6.3576 |
| 0.5 | 19242 | 8.5107 |
| 0.6 | 25396 | 11.2326 |
| 0.7 | 30617 | 13.5418 |
| 0.8 | 36468 | 16.1297 |
| 0.9 | 86720 | 38.3561 |
| 1.0 | 529 | 0.2340 |
| Total | 226092 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 165097 | 73.4698 |
| 0.1 | 15983 | 7.1126 |
| 0.2 | 11003 | 4.8964 |
| 0.3 | 7819 | 3.4795 |
| 0.4 | 7010 | 3.1195 |
| 0.5 | 5253 | 2.3376 |
| 0.6 | 4657 | 2.0724 |
| 0.7 | 4013 | 1.7858 |
| 0.8 | 2553 | 1.1361 |
| 0.9 | 1326 | 0.5901 |
| Total | 224714 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 14815 | 6.5928 |
| 0.4 | 17220 | 7.6631 |
| 0.5 | 21614 | 9.6184 |
| 0.6 | 27429 | 12.2062 |
| 0.7 | 31687 | 14.1010 |
| 0.8 | 36159 | 16.0911 |
| 0.9 | 75353 | 33.5328 |
| 1.0 | 437 | 0.1945 |
| Total | 224714 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 388373 | 74.7153 |
| 0.1 | 34404 | 6.6186 |
| 0.2 | 24193 | 4.6543 |
| 0.3 | 18285 | 3.5177 |
| 0.4 | 13582 | 2.6129 |
| 0.5 | 11829 | 2.2757 |
| 0.6 | 10416 | 2.0038 |
| 0.7 | 9853 | 1.8955 |
| 0.8 | 5741 | 1.1045 |
| 0.9 | 3128 | 0.6018 |
| Total | 519804 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 40783 | 7.8458 |
| 0.4 | 48323 | 9.2964 |
| 0.5 | 56618 | 10.8922 |
| 0.6 | 64986 | 12.5020 |
| 0.7 | 68820 | 13.2396 |
| 0.8 | 77624 | 14.9333 |
| 0.9 | 161733 | 31.1142 |
| 1.0 | 917 | 0.1764 |
| Total | 519804 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering